FMO DATABASE

FMODB ID: 63QRZ

Calculation Name: 1T39-A-Xray310

Preferred Name: 6-O-methylguanine-DNA methyltransferase

Target Type: SINGLE PROTEIN

Ligand Name: phosphoric acid mono-[5-(1-ethyl-2,6-dioxo-1,2,3,6-tetrahydro-purin-9-yl)-3-hydroxy-tetrahydro-furan-2-ylmethyl]ester

ligand 3-letter code: E1X

PDB ID: 1T39

Chain ID: A

ChEMBL ID: CHEMBL2864

UniProt ID: P16455

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1422127.85272
FMO2-HF: Nuclear repulsion	1363069.933148
FMO2-HF: Total energy	-59057.919572
FMO2-MP2: Total energy	-59228.262226

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE )

Summations of interaction energy for fragment #1(A:4:ACE )

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
1.898	4.502	0.282	-1.138	-1.748	-0.006

Interaction energy analysis for fragmet #1(A:4:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.075 / q_NPA : 0.029

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	6	GLU	-1	-0.858	-0.927	3.856	0.593	1.683	-0.005	-0.505	-0.580	-0.001
4	A	7	MET	0	-0.075	-0.027	6.407	0.126	0.126	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.947	0.993	8.687	0.341	0.341	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.944	0.955	10.998	0.231	0.231	0.000	0.000	0.000	0.000
7	A	10	THR	0	0.033	0.036	14.391	0.044	0.044	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.014	-0.014	16.071	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.022	0.003	19.726	0.005	0.005	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.939	-0.967	22.100	-0.073	-0.073	0.000	0.000	0.000	0.000
11	A	14	SER	0	0.069	0.047	25.673	0.000	0.000	0.000	0.000	0.000	0.000
12	A	15	PRO	0	0.022	0.011	27.464	0.002	0.002	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.038	-0.019	28.183	0.003	0.003	0.000	0.000	0.000	0.000
14	A	17	GLY	0	0.001	0.015	29.265	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.888	0.927	24.584	0.075	0.075	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.034	-0.026	22.214	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.939	-0.974	18.168	-0.209	-0.209	0.000	0.000	0.000	0.000
18	A	21	LEU	0	0.016	0.012	15.846	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.003	0.007	13.634	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	23	GLY	0	0.060	0.002	10.758	0.020	0.020	0.000	0.000	0.000	0.000
21	A	24	CYS	0	-0.128	0.011	5.453	-0.212	-0.212	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.915	-0.962	2.856	-0.334	0.953	0.287	-0.600	-0.974	-0.005
23	A	26	GLN	0	0.078	0.018	4.736	0.298	0.525	0.000	-0.033	-0.194	0.000
24	A	27	GLY	0	-0.014	-0.062	5.639	0.537	0.537	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.058	-0.030	9.233	-0.083	-0.083	0.000	0.000	0.000	0.000
26	A	29	HIS	0	-0.060	-0.041	11.378	0.094	0.094	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.968	-0.998	13.407	-0.188	-0.188	0.000	0.000	0.000	0.000
28	A	31	ILE	0	0.011	0.002	16.453	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.974	1.012	19.228	0.162	0.162	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.033	0.007	22.261	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	LEU	0	-0.141	-0.056	23.145	0.007	0.007	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.046	0.022	26.387	0.004	0.004	0.000	0.000	0.000	0.000
33	A	36	NME	0	0.018	0.021	28.874	0.002	0.002	0.000	0.000	0.000	0.000
34	A	55	ACE	0	0.013	-0.006	8.339	0.018	0.018	0.000	0.000	0.000	0.000
35	A	56	PRO	0	-0.001	0.029	7.016	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	57	GLU	-1	-0.907	-0.981	8.066	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	58	PRO	0	0.023	0.016	7.924	0.042	0.042	0.000	0.000	0.000	0.000
38	A	59	LEU	0	0.033	0.030	10.052	0.075	0.075	0.000	0.000	0.000	0.000
39	A	60	MET	0	-0.008	0.019	12.251	0.061	0.061	0.000	0.000	0.000	0.000
40	A	61	GLN	0	0.046	0.034	12.833	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	62	CYS	0	-0.058	-0.033	14.685	0.032	0.032	0.000	0.000	0.000	0.000
42	A	63	THR	0	-0.033	-0.052	16.036	0.027	0.027	0.000	0.000	0.000	0.000
43	A	64	ALA	0	-0.013	0.003	18.024	0.018	0.018	0.000	0.000	0.000	0.000
44	A	65	TRP	0	0.066	0.044	19.459	0.006	0.006	0.000	0.000	0.000	0.000
45	A	66	LEU	0	0.008	0.001	20.158	0.011	0.011	0.000	0.000	0.000	0.000
46	A	67	ASN	0	-0.010	-0.016	22.309	0.012	0.012	0.000	0.000	0.000	0.000
47	A	68	ALA	0	0.015	0.023	23.877	0.009	0.009	0.000	0.000	0.000	0.000
48	A	69	TYR	0	-0.057	-0.054	25.133	0.005	0.005	0.000	0.000	0.000	0.000
49	A	70	PHE	0	-0.042	-0.042	25.295	0.006	0.006	0.000	0.000	0.000	0.000
50	A	71	HIS	0	-0.031	-0.022	27.414	0.008	0.008	0.000	0.000	0.000	0.000
51	A	72	GLN	0	-0.014	0.002	28.189	0.006	0.006	0.000	0.000	0.000	0.000
52	A	73	PRO	0	-0.001	0.013	29.421	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	74	GLU	-1	-0.972	-0.995	30.482	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	75	ALA	0	0.022	0.014	29.342	0.003	0.003	0.000	0.000	0.000	0.000
55	A	76	ILE	0	0.012	0.014	24.501	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	77	GLU	-1	-0.988	-1.001	24.786	-0.076	-0.076	0.000	0.000	0.000	0.000
57	A	78	GLU	-1	-1.011	-0.991	24.850	-0.041	-0.041	0.000	0.000	0.000	0.000
58	A	79	PHE	0	-0.050	-0.024	21.314	0.000	0.000	0.000	0.000	0.000	0.000
59	A	80	PRO	0	-0.040	-0.006	17.265	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	81	VAL	0	0.009	-0.009	17.804	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	82	PRO	0	0.000	0.008	13.300	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	83	ALA	0	0.018	0.019	10.083	0.017	0.017	0.000	0.000	0.000	0.000
63	A	84	LEU	0	-0.001	0.004	12.069	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	85	HIS	0	-0.003	0.018	9.109	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	86	HIS	0	0.134	0.059	11.221	0.004	0.004	0.000	0.000	0.000	0.000
66	A	87	PRO	0	0.004	-0.009	14.154	0.034	0.034	0.000	0.000	0.000	0.000
67	A	88	VAL	0	-0.052	-0.026	16.280	0.035	0.035	0.000	0.000	0.000	0.000
68	A	89	PHE	0	-0.007	-0.018	15.583	0.040	0.040	0.000	0.000	0.000	0.000
69	A	90	GLN	0	-0.041	-0.012	11.717	-0.068	-0.068	0.000	0.000	0.000	0.000
70	A	91	GLN	0	0.020	0.031	15.708	0.021	0.021	0.000	0.000	0.000	0.000
71	A	92	GLU	-1	-0.884	-0.947	19.228	-0.125	-0.125	0.000	0.000	0.000	0.000
72	A	93	SER	0	0.012	-0.008	22.426	0.012	0.012	0.000	0.000	0.000	0.000
73	A	94	PHE	0	0.047	0.010	25.081	0.001	0.001	0.000	0.000	0.000	0.000
74	A	95	THR	0	0.010	-0.019	23.813	0.005	0.005	0.000	0.000	0.000	0.000
75	A	96	ARG	1	0.909	0.984	18.007	0.179	0.179	0.000	0.000	0.000	0.000
76	A	97	GLN	0	0.058	0.035	23.226	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	98	VAL	0	-0.011	-0.004	25.591	0.001	0.001	0.000	0.000	0.000	0.000
78	A	99	LEU	0	0.021	0.019	21.945	0.004	0.004	0.000	0.000	0.000	0.000
79	A	100	TRP	0	0.035	0.003	16.554	0.001	0.001	0.000	0.000	0.000	0.000
80	A	101	LYS	1	0.881	0.931	23.141	0.090	0.090	0.000	0.000	0.000	0.000
81	A	102	LEU	0	-0.009	-0.019	26.219	0.008	0.008	0.000	0.000	0.000	0.000
82	A	103	LEU	0	0.038	0.027	20.508	0.004	0.004	0.000	0.000	0.000	0.000
83	A	104	LYS	1	0.894	0.963	20.323	0.135	0.135	0.000	0.000	0.000	0.000
84	A	105	VAL	0	-0.078	-0.044	26.077	0.009	0.009	0.000	0.000	0.000	0.000
85	A	106	VAL	0	-0.018	0.014	29.004	0.006	0.006	0.000	0.000	0.000	0.000
86	A	107	LYS	1	0.985	0.998	28.981	0.056	0.056	0.000	0.000	0.000	0.000
87	A	108	PHE	0	0.017	-0.015	29.677	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	109	GLY	0	0.056	0.044	31.060	0.005	0.005	0.000	0.000	0.000	0.000
89	A	110	GLU	-1	-0.934	-0.968	33.337	-0.060	-0.060	0.000	0.000	0.000	0.000
90	A	111	VAL	0	0.021	0.004	34.104	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	112	ILE	0	-0.033	-0.015	32.530	0.003	0.003	0.000	0.000	0.000	0.000
92	A	113	SER	0	0.018	0.017	35.582	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	114	TYR	0	0.015	-0.004	34.409	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	115	GLN	0	-0.020	-0.027	35.063	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	116	GLN	0	0.073	0.026	36.623	0.000	0.000	0.000	0.000	0.000	0.000
96	A	117	LEU	0	-0.002	0.008	29.214	0.001	0.001	0.000	0.000	0.000	0.000
97	A	118	ALA	0	0.007	-0.008	32.749	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	119	ALA	0	-0.027	0.000	34.102	0.001	0.001	0.000	0.000	0.000	0.000
99	A	120	LEU	0	0.009	0.019	31.271	0.000	0.000	0.000	0.000	0.000	0.000
100	A	121	ALA	0	-0.102	-0.043	29.792	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	122	GLY	0	0.008	0.003	30.865	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	123	ASN	0	-0.003	-0.019	33.555	0.007	0.007	0.000	0.000	0.000	0.000
103	A	124	PRO	0	0.097	0.055	35.543	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	125	LYS	1	0.898	0.953	37.981	0.044	0.044	0.000	0.000	0.000	0.000
105	A	126	ALA	0	-0.018	-0.011	35.208	0.000	0.000	0.000	0.000	0.000	0.000
106	A	127	ALA	0	0.096	0.046	34.998	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	128	ARG	1	0.976	0.979	35.099	0.055	0.055	0.000	0.000	0.000	0.000
108	A	129	ALA	0	0.000	0.006	32.371	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	130	VAL	0	0.045	0.021	30.877	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	131	GLY	0	0.043	0.025	31.004	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	132	GLY	0	-0.068	-0.043	30.667	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	133	ALA	0	-0.020	-0.007	27.390	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	134	MET	0	0.008	0.004	26.427	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	135	ARG	1	0.915	0.972	27.077	0.093	0.093	0.000	0.000	0.000	0.000
115	A	136	GLY	0	-0.033	-0.011	24.872	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	137	ASN	0	-0.005	-0.024	22.642	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	138	PRO	0	-0.015	0.015	18.451	0.009	0.009	0.000	0.000	0.000	0.000
118	A	139	VAL	0	0.034	-0.012	17.266	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	140	PRO	0	0.043	0.032	20.406	0.017	0.017	0.000	0.000	0.000	0.000
120	A	141	ILE	0	-0.014	0.003	22.989	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	142	LEU	0	-0.006	-0.010	17.781	0.004	0.004	0.000	0.000	0.000	0.000
122	A	143	ILE	0	-0.042	-0.007	20.389	0.010	0.010	0.000	0.000	0.000	0.000
123	A	144	PRO	0	0.024	0.008	23.614	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	145	CYS	0	-0.053	-0.026	26.873	0.005	0.005	0.000	0.000	0.000	0.000
125	A	146	HIS	0	-0.051	-0.068	28.303	0.001	0.001	0.000	0.000	0.000	0.000
126	A	147	ARG	1	0.850	0.926	28.472	0.091	0.091	0.000	0.000	0.000	0.000
127	A	148	VAL	0	-0.019	0.004	31.050	0.006	0.006	0.000	0.000	0.000	0.000
128	A	149	VAL	0	0.012	-0.005	33.689	0.001	0.001	0.000	0.000	0.000	0.000
129	A	150	CYS	0	-0.054	-0.035	37.307	0.000	0.000	0.000	0.000	0.000	0.000
130	A	151	SER	0	0.063	0.018	39.975	0.000	0.000	0.000	0.000	0.000	0.000
131	A	152	SER	0	-0.057	-0.019	42.292	0.001	0.001	0.000	0.000	0.000	0.000
132	A	153	GLY	0	0.049	0.037	43.488	0.002	0.002	0.000	0.000	0.000	0.000
133	A	154	ALA	0	0.006	0.010	43.137	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	155	VAL	0	0.081	0.039	37.417	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	156	GLY	0	-0.078	-0.056	37.911	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	157	ASN	0	0.032	0.023	35.478	0.003	0.003	0.000	0.000	0.000	0.000
137	A	158	TYR	0	0.045	-0.002	28.280	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	159	SER	0	-0.010	-0.005	28.209	0.006	0.006	0.000	0.000	0.000	0.000
139	A	160	GLY	0	0.003	0.018	29.483	0.002	0.002	0.000	0.000	0.000	0.000
140	A	161	GLY	0	0.039	0.018	30.239	0.004	0.004	0.000	0.000	0.000	0.000
141	A	162	LEU	0	-0.022	-0.017	33.753	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	163	ALA	0	0.031	0.013	35.715	0.001	0.001	0.000	0.000	0.000	0.000
143	A	164	VAL	0	0.046	0.020	29.810	0.002	0.002	0.000	0.000	0.000	0.000
144	A	165	LYS	1	0.840	0.950	33.102	0.077	0.077	0.000	0.000	0.000	0.000
145	A	166	GLU	-1	-0.910	-0.958	34.104	-0.054	-0.054	0.000	0.000	0.000	0.000
146	A	167	TRP	0	0.064	0.029	31.218	0.000	0.000	0.000	0.000	0.000	0.000
147	A	168	LEU	0	0.011	0.011	29.259	0.001	0.001	0.000	0.000	0.000	0.000
148	A	169	LEU	0	-0.024	-0.017	33.104	0.002	0.002	0.000	0.000	0.000	0.000
149	A	170	ALA	0	-0.024	-0.026	35.756	0.003	0.003	0.000	0.000	0.000	0.000
150	A	171	HIS	0	-0.027	-0.002	31.388	0.005	0.005	0.000	0.000	0.000	0.000
151	A	172	GLU	-1	-0.725	-0.823	30.979	-0.080	-0.080	0.000	0.000	0.000	0.000
152	A	173	GLY	0	-0.044	-0.007	35.123	0.003	0.003	0.000	0.000	0.000	0.000
153	A	174	HIS	0	-0.039	-0.012	37.069	0.003	0.003	0.000	0.000	0.000	0.000
154	A	175	ARG	1	0.919	0.936	40.783	0.036	0.036	0.000	0.000	0.000	0.000
155	A	176	NME	0	0.020	0.032	43.492	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE )